San Francisco 49ers quarterback Colin Kaepernick runs for a 56-yard touchdown against the Green Bay Packers in San Francisco Saturday.

SANTA CLARA, Calif. — Despite all those gaudy statistics and impressive physical skills, Colin Kaepernick faced plenty of questions coming out of Nevada about whether he was the product of a gimmicky college offense that would have no chance of working in the pros.

On the big stage of the NFL playoffs, Kaepernick is demonstrating just what he and that pistol offense are capable of against the toughest competition.

With scintillating runs in the option game and downfield passes with his powerful right arm, Kaepernick has the San Francisco 49ers back in the NFC championship game for a second straight year and has given more credibility to the offense designed by his college coach less than a decade ago.

“At first they said, that’s just a college offense,” said former Nevada coach Chris Ault, who invented the offense and used it in college with Kaepernick. “Lo and behold, somebody came out and said you can do that in the NFL every so often. The NFL has been such a copycat league. The formation has expanded the landscape of football collegiately and pro-wise. The pros see advantages of what you can do with these mobile quarterbacks in the pistol.”

Never had it been more effective than it was in San Francisco’s 45-31 win last week against Green Bay. Kaepernick set a quarterback record with 181 yards rushing on 16 carries, scoring on a 20-yard scramble and 56-yard sprint off a zone read play. He also threw for 263 yards and two touchdowns, exploiting whatever opening the Packers gave him.

“The one thing it does is it kind of makes you a little bit indecisive in what you want to do,” Green Bay defensive back Charles Woodson said. “You want to shoot in there but he may hold the ball and take it outside. If you go outside he might give it to the running back and take it up the middle. It’s one of those things that makes you play flat-footed a little bit.”

Kaepernick is far from alone in running a style of offense that until only recently was dismissed by many in the NFL as unsuitable for the pro game. Cam Newton has successfully used the zone read in Carolina to post prolific numbers the past two seasons and rookies Robert Griffin III in Washington and Russell Wilson in Seattle used elements of the pistol and the read option game to get their teams to the playoffs.

Their success has helped remove the stigma that running quarterbacks can’t succeed in the NFL.

“I think quarterbacks that have a talent for running the ball can be very effective,” 49ers coach Jim Harbaugh said. “That’s been long known in football, the National Football League as well. A quarterback that can get out of the pocket, run, pick up first downs, that’s a threat that the defense has to account for. There are some quarterback-driven runs that have been added because our quarterbacks are very good at those, and Colin especially.”

Hall of Famer Steve Young calls the offense a bridge to help athletic quarterbacks with limited pocket experience transition from college to the pros, but said it is still essential to be able to beat defenses from the pocket.

That’s where quarterbacks like Kaepernick, Griffin and Wilson have the advantage over Tim Tebow, who used the zone read to great success last season in Denver but is struggling to get playing time because of his erratic throwing.

Kaepernick prides himself on his ability to do it all, dismissing the question of whether he’s a running or throwing quarterback.

“I don’t want to be categorized,” Kaepernick said.

Ault implemented the offense at Nevada in 2005, hoping to combine elements of the spread passing game from the shotgun with the power running game. The offense got its name — the pistol — because the quarterback lines up about 4 yards behind center as opposed to about 6 in the shotgun.

With the running back behind the quarterback instead of by his side in the shotgun, traditional running plays are easier to execute because the back is moving toward the line of scrimmage when he gets the ball rather than horizontally.

The offense began to evolve when Kaepernick took over in 2007. Late that season, Ault began mixing in some of the zone read plays where the quarterback puts the ball in the belly of the running back and then reads the defense to decide whether to go through with the handoff or keep the ball and run outside if the defensive end reacts to the running back.

Exposing the quarterbacks to hits running the ball is a big reason why NFL teams are hesitant to use the system so much, with Griffin’s latest injury a prime example.

“I know you can’t run the quarterback in the NFL as much as we do in college,” Ault said. “I agree with that. But I’ve seen quarterbacks take as many vicious hits dropping back 40 times a game as running the pistol.”

Soon, coaches from high school, college, Canada and the NFL made trips to Reno to learn more about the offense. San Francisco offensive coordinator Greg Roman was one of those in 2009 while he was still at Stanford. Roman used a few of the plays with Andrew Luck at Stanford but really started utilizing them once Kaepernick took over from Alex Smith halfway through this season.

The Niners have added new wrinkles with tight ends in the backfield, more play-action out of the pistol and different motions to deceive the defense.

“It’s a nightmare, especially when you have a guy who can run 4.4, 4.3, a guy who can outrun defensive backs or linebackers,” Niners safety Donte Whitner said. “You really don’t know where the football is going against this read-option stuff. You really don’t know until you finally see it. Sometimes he can pull it back, drop back and throw it deep. You really have to respect all of the weapons and be disciplined. It’s tough to do it for four quarters against a quarterback like that.”